LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
########################################################################
### Pure diffusion with a reaction source term analog of a periodic  ###
### Poiseuille flow problem using transport DPD (tDPD) simulation    ###
###                                                                  ###
### Created  : Zhen Li (zhen_li@brown.edu)                           ###
###            Division of Applied Mathematics, Brown University.    ###
###                                                                  ###
### tDPD system setup follows Fig.1 in the publication:              ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis.          ###
### "Transport dissipative particle dynamics model for mesoscopic    ###
### advection-diffusion-reaction problems. J. Chem. Phys.,           ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254                        ###
########################################################################
units                   lj
dimension               3
boundary                p p p
neighbor                0.2 bin
neigh_modify        every 1 delay 0 check yes

atom_style              tdpd 2
comm_modify  vel yes

region     tdpd     block -10 10 -10 10 -5 5 units box
create_box          1 tdpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
  2 by 2 by 1 MPI processor grid
create_atoms        1 random 16000 276438 NULL
Created 16000 atoms
  using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
  create_atoms CPU = 0.002 seconds
mass                1 1.0
set                 atom * cc 1 1.0
Setting atom values ...
  16000 settings made for cc index 1
set                 atom * cc 2 1.0
Setting atom values ...
  16000 settings made for cc index 2

pair_style          tdpd 1.0 1.58 9872598
pair_coeff          1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0

compute             mythermo all temp
thermo              50
thermo_modify       temp mythermo
thermo_modify       flush yes

velocity            all create 1.0 432982 loop local dist gaussian

fix         mvv     all mvv/tdpd 0.5
fix         upper1  all tdpd/source 1 cuboid 0.0  5.0 0.0 20.0 10.0 10.0  0.01
fix         lower1  all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix         upper2  all tdpd/source 2 cuboid 0.0  5.0 0.0 20.0 10.0 10.0 -0.01
fix         lower2  all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0  0.01

timestep            0.01
run                 500

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair tdpd command: doi:10.1063/1.4923254

@Article{ZLi2015_JCP,
 author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G. E.},
 title = {Transport Dissipative Particle Dynamics Model for Mesoscopic Advection-Diffusion-Reaction Problems},
 journal = {The Journal of Chemical Physics},
 year = {2015},
 volume = {143},
 number = {1},
 pages = {014101}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.78
  ghost atom cutoff = 1.78
  binsize = 0.89, bins = 23 23 12
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair tdpd, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.337 | 5.351 | 5.36 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   1              48.942039      0              50.441946      199.59508    
        50   1.0164166      43.95706       0              45.48159       198.02944    
       100   0.99583217     43.760777      0              45.254431      198.26943    
       150   1.0025022      43.730114      0              45.233774      198.402      
       200   0.99563635     43.72379       0              45.217151      197.6948     
       250   1.0117752      43.724349      0              45.241917      195.70427    
       300   0.98950567     43.72333       0              45.207496      197.582      
       350   0.99351667     43.719413      0              45.209595      194.69504    
       400   1.0050663      43.715857      0              45.223362      198.50199    
       450   1.003148       43.712337      0              45.216965      196.26462    
       500   0.99888463     43.712357      0              45.21059       195.78645    
Loop time of 16.464 on 4 procs for 500 steps with 16000 atoms

Performance: 26239.140 tau/day, 30.369 timesteps/s, 485.910 katom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 14.166     | 14.302     | 14.373     |   2.1 | 86.87
Neigh   | 1.406      | 1.4132     | 1.4179     |   0.4 |  8.58
Comm    | 0.53805    | 0.61257    | 0.75493    |  10.7 |  3.72
Output  | 0.00041375 | 0.00062178 | 0.00091415 |   0.0 |  0.00
Modify  | 0.088249   | 0.089209   | 0.090198   |   0.2 |  0.54
Other   |            | 0.04683    |            |       |  0.28

Nlocal:           4000 ave        4013 max        3992 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost:           5990 ave        6012 max        5980 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs:         187350 ave      188412 max      186633 min
Histogram: 1 0 1 1 0 0 0 0 0 1

Total # of neighbors = 749401
Ave neighs/atom = 46.837562
Neighbor list builds = 182
Dangerous builds = 0
reset_timestep      0

compute     cc1     all tdpd/cc/atom 1
compute     cc2     all tdpd/cc/atom 2
compute     bin     all chunk/atom bin/1d y 0.0 1.0
fix         stat    all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile

run                 100
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.588 | 5.602 | 5.61 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0.99888463     43.712357      0              45.21059       197.42728    
        50   1.0015386      43.71567       0              45.217884      198.28372    
       100   1.0053363      43.718221      0              45.226131      195.45072    
Loop time of 3.09095 on 4 procs for 100 steps with 16000 atoms

Performance: 27952.588 tau/day, 32.353 timesteps/s, 517.641 katom-step/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.6867     | 2.6999     | 2.7131     |   0.8 | 87.35
Neigh   | 0.2523     | 0.25332    | 0.25501    |   0.2 |  8.20
Comm    | 0.087738   | 0.10048    | 0.11401    |   4.0 |  3.25
Output  | 0.00014184 | 0.00015461 | 0.00015946 |   0.0 |  0.01
Modify  | 0.028066   | 0.028154   | 0.02831    |   0.1 |  0.91
Other   |            | 0.008906   |            |       |  0.29

Nlocal:           4000 ave        4024 max        3988 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost:           5977 ave        6004 max        5941 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs:         187313 ave      188798 max      186723 min
Histogram: 2 1 0 0 0 0 0 0 0 1

Total # of neighbors = 749253
Ave neighs/atom = 46.828313
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:19
